Heartwarming: The Legend of Zelda: Phantom Hourglass
The ending of The Legend of Zelda: Phantom Hourglass: It appears it was All Just a Dream, but then Link finds the titular Hourglass and rushes to the other side of the ship JUST IN TIME to see Linebeck's ship on the horizon. (The music probably didn't help, either.) Just imagine it now, how Linebeck must have been looking back to Link, saying "You did good, kid."
As divergent from the game as the manga of Phantom Hourglass was, they still did good with the scene where Linebeck is possessed by Bellum. He would rather kill himself than attack Link, and it's the only means of defiance he has.
At some point during the game, you get a letter in the mail from Linebeck. Seems strange at first since he's always travelling with Link, until the letter reveals that despite the way he usually acts, Linebeck really is grateful towards Link. He just finds it hard to actually say that to him.
